If the Input raster or feature zone data (in_zone_data in Python) parameter value is a feature, for any of the zone features that do not overlap any cell centers of the value raster, those zones will not be converted to the internal zone raster. As a result, those zones will not be represented in the output.
Ensure that each of your zones contains one or more cell centers. You can create more cell centers by specifying a smaller cell size in the environment. The default analysis cell size comes from the value raster. Therefore, specifying a Cell Size that is smaller than that of the value raster will enable more zones to be captured. Keep in mind that specifying a smaller cell size will generate a larger output raster. More importantly, the higher resolution output may give the wrong perception of a higher quality result than what it actually is, since the additional detail does not actually exist in the input value raster.